title: PASFIF-R HiChIP

city: New York

first: Sonali

last: Narang

address: 435 east 30th street

institute: NYU Langone

data_processing:
hic-bench platform
Reads filtered for accepted intra-chromosomal read-pairs by the GenomicTools tools-hic filter command in the hic-bench platform
Interaction matrices for each chromosome separately were created by the hic-bench platform at 40kb resolution
Filtered read counts were normalized by iterative correction and eigenvector decomposition
To account for variances in read counts of more distant loci, distance normalization for each chromosome matrix was performed.
Assembly: hg19
Supplementary files format and content: .hic files consisting of hic signal
Library strategy: H3K27ac Hi-ChIP

source_name: primary bone marrow

growth_protocol: Cryopreserved paired diagnosis/relapse primary patient bone marrow samples from individual patients were obtained from the Children’s Oncology group (COG) ALL biorepository or St. Jude Children’s Research Hospital.

extract_protocol:
Following FACS, leukemic cells were immediately fixed and crosslinked with 2% formaldehyde at room temperature for 10 minutes. Glycine was added to stop the reaction. Crosslinked cells were washed with PBS and then frozen on dry ice. Crosslinked cell pellets were stored at -80 until ready for processing.
HiChIP libraries were generated using the Arima-HiC+ kit (A410232) with Swift Biosciences® Accel-NGS® 2S Plus DNA Library Kit (Cat # 21024) and Indexing kit (Cat # 26148) according to manufacturer’s protocol with minor modifications.

tag: disease state

value: B-ALL

value: primary bone marrow

value: Relapse


title: ArD_0h _1

status: Public on May 01 2024

type: SRA

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

country: China

institute: College of Life Sciences, Tianjin Normal University

library_source: genomic

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2).
These reads were aligned to the Artemia genome using BWA, with standard parameters.
These reads were then filtered for high quality with MAPQ≥13 (i.e. p≤0.05), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt).
FastAC was used to evaluate the quality of the data.
Macs2 software was used for peak calling.
Supplementary files format and content: raw count,RPM values,gene ID and transcript ID for each peak

molecule: genomic DNA

organism: Artemia parthenogenetic lineage

source_name: cyst

growth_protocol: Artemia parthenogenetica cysts (provided by Asian Regional Artemia Reference Center, ARARC) were collected in Ebinur Lake and reactivated after dehydration and refrigeration treatment to break diapause.

extract_protocol:
nuclei were extracted from each sample, and the nuclei pellet was re-suspended in the Tn5 transposase reaction mix.The transposition reaction was incubated at 37°C for 30 min. Equimolar adapter 1 and adapter 2 were added after transposition.
PCR was then performed to amplify the libraries. After the PCR amplification, libraries were purified with the AMPure beads and the quality of libraries was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

treatment_protocol: For diapause stage and 5 h after diapause breaking, the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 28 °C under continuous illumination. Each sample was quickly collected and put in liquid nitrogen immediately and then preserved in a −80 °C refrigerator.

tag: tissue

value: cyst

tag: cell line

value: Artemia parthenogenetica

tag: cell type

tag: genotype

value: WT

tag: treatment

value: no treatment


title: ArD_0h _2


title: Sample 25_SF7761, ChIP-seq H3.3K27M, DMSO

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

data_processing:
RNAseq: The sequenced paired-end reads were mapped to hg38 genome using tophat2 aligner v2.1.1 with the default parameters. The expression estimates for each gene were obtained using Bioconductor package DESeq2. TPM (Transcripts per Kilobase Million) values were calculated
ChIPseq: The paired-end fragments were generated. Reads were mapped to the to hg38 genome using Bowtie aligner version 0.12.9. Only uniquely mapped reads were retained. The reads with insert sizes <50 bp or >500 bp were removed from further analysis. Genomic positions with the numbers of mapped tags above the significance threshold of Z-score of 7 were identified as anomalous, and the tags mapped to such positions were discarded. H2A.Z, H3.3 and H3.3K27M occupancies were estimated as tag frequencies
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each RNA-seq sample
Supplementary files format and content: ChIPseq: wig files with coverage

organism: Homo sapiens

source_name: brain

extract_protocol:
RNA-seq: RNA was isolated using RNeasy Plus Kit (Qiagen) according to manufacturer’s instructions and the quality was assessed with the Agilent 2100 Bioanalyzer with an RNA 6000 Pico Kit (Agilent Technologies).
RNA-seq: PolyA-enriched RNA libraries were prepared with the KAPA Stranded mRNA Sample Preparation Kit (Kapa Biosystems).
ChIP-seq: ChIP-seq (including crosslinikng, cell lysis, chromatin digestion with Mnase, and chromatin immunoprecipitatation with H3.3 and H3.3K27M antibodies) was performed based on protocol by Cook et al.., 2017 (doi: 10.1002/cpmb.45). Eluted and input DNA was purified with phenol-chloroform extraction followed by additional purification with ZymoResearch DNA Clean & Concentrator-5 columns. Digested DNA profiles were confirmed using the 2100 Bioanalyzer with the Agilent DNA High Sensitivity chip (Agilent Technologies).
ChIP-seq: The Input and ChIP libraries were prepared using the Qiaseq Ultra Low Input Library Kit (Qiagen), according to manufacturer’s instructions.

value: brain

tag: antibody

value: H3.3K27M mutant

value: DMSO


title: PASFIF-D HiChIP

state: NY

country: USA

value: Diagnosis


title: Sample 26_SF7761, ChIP-seq H3.3K27M, SB939


title: Exp#1_Bre1_RIP_0317

city: Taiepi

first: Ming-Chia

last: Lee

address: Library, Info & Research Bldg, Rm 904 #155, Sec. 2, Li-Nong St

department: Department of Life Sciences and Institute of Genome Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

library_source: transcriptomic

data_processing:
For Exp#1, sequenced reads were trimmed for adaptor sequence, and mapped to dm6 whole genome using tophat (Bowtie2 [2.0.6.0] and Samtools [0.1.18.0]); For Exp#2, sequenced reads were trimmed for adaptor sequence, and mapped to dm6 whole genome using CLC Genomics Workbench 11.0.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.
Assembly: dm6

molecule: total RNA

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Oregon-R flies were raised under standard fly culture condition. For each RIP experiment, ~200 young females (12hr post eclosion) were collected for dissecting out oavries.

extract_protocol:
Collected ovaries were transferred into RIP buffer and then homogenized, lysed, and centrifuged to acquire ovarian lysate.
Library was prepared using iIlumina TruSeq RNA Sample Prep Kit v2 (Guide Revision F). The polyA selection steps were skipped, and samples were proceed directly to Fragmentation and Priming and cDNA synthesis.

treatment_protocol: Ovarian lysate collected from young females was spited into three parts for adding anti-IgG, anti-Lsd1 and anti-Bre1 antibody respectively.

value: Ovary

tag: strain

value: Oregon-R

value: wild type


title: ArR_5h_2

value: the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 29 °C under continuous illumination.


title: PASPNY-R RNA-seq

data_processing:
Slide-n-Seq (sns) pipeline: https://igordot.github.io/sns/
Patient RNA-seq fastq files were processed in single replicates using the routes “rna-star” and “rna-star-groups-dge”
adapters and low quality bases were trimmed using trimmomatic
data was aligned to reference genome (hg19) using STAR
Genes-samples count matrices were generated using featureCounts
Assembly: hg19
Supplementary files format and content: bigwig files and comma-separated values files including raw and TPM values for each sample

growth_protocol: Cryopreserved paired diagnosis/relapse primary patient bone marrow samples from individual patients were obtained from the Children’s Oncology group (COG) ALL biorepository or St. Jude Children’s Research Hospital. Following FACS, 50,000-200,000 leukemic cells were immediately resuspended in Buffer RLT plus BME and frozen on dry ice.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Micro Kit
RNAseq libraries were generated by the NYU Genome Technology Center using the Low input Clontech SMART-Seq kit


title: C6 offshore to offshore, treatment [high_C6_off]

city: Miammi

first: Catalina

last: Aguilar

state: Florida

address: 4600 Rickenbacker Causeway

department: Rosenstiel School of Marine, Atmospheric & Earth Science

institute: University of Miami

description:
high_C6_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S20

data_processing:
Adapters and low-quality reads were removed in Trimmomatic v0.36 (phred33, quality score > 20, 4 bp sliding window; Bolger, Lohse, and Usadel 2014)
The metatranscriptome was filtered by performing BLASTx (e-value < 1e−5) searches against two coral proteomes, and BLASTn (e-value < 1e−5) searches against four Symbiodiniaceae genomes (as of June, 2018) (coral: Acropora digifitera and Orbicella faveolata. Symbiodiniaceae: Symbiodinium microadriaticum; Breviolum minutum; Cladocopium goreaui; Durusdinium trenchii).
Trinity scripts (Grabherr et al., 2011) were used to map the reads back to both transcriptomes using the alignment-based abundance estimation method RSEM (RNA-Seq by Expectation-Maximization) and to build an expression matrix from the transcript abundance files.
Assembly: Trinity scripts (Grabherr et al., 2011)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Orbicella faveolata

source_name: coral tissue

extract_protocol:
Total RNA was extracted using the total RNAqueous kit (AM1912, Life Technologies), according to the manufacturer’s instructions
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit following the manufacturer’s protocol at the Duke Center for Genomic and Computational Biology

treatment_protocol: Following acclimation, temperatures were gradually increased at different rates over an additional seven days to reach an elevated temperatures (32C), or control (30C). Samples were keep at this treatment for 6 days and then collected for RNAseq.

value: coral tissue

tag: origin

value: off

tag: transplant

value: Offshore

tag: collection site


title: Sample 17_SF7761, ChIP-seq H3.3, DMSO


title: Sample 18_SF7761, ChIP-seq H3.3, SB939


title: PASPNY-D RNA-seq

value: B-ALL

value: primary bone marrow


title: C5 offshore to offshore, treatment [high_C5_off]

description:
high_C5_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S56


title: Exp#1_IgG_RIP_0317

value: anti-IgG


title: C4 offshore to offshore, treatment [high_C4_off]

description:
high_C4_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S42


title: PASMEN-D RNA-seq


title: Sample 9_SF7761, ChIP-seq H2A.Z, DMSO


title: C3 offshore to offshore, treatment [high_C3_off]

description:
high_C3_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S23


title: 111T_Micro3,Rhesus Macauqe,control,non-infection

city: Omaha

first: Howard

middle: S

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: Mmul10, NCBI RefSeq assembly and SIVmac251
Supplementary files format and content: FASTQ files contain the sequenced data
Supplementary files format and content: H5 files contain feature and cell barcode matrix

organism: Macaca mulatta

source_name: Brain

extract_protocol:
Brains were removed at necropsy, microglia/macrophage enriched cells were isolated from the cryopreserved brains (104T, 111T) and fresh brains (92T, 93T, 94T, 95T). Isolates were immunomagnetically enriched for CD45+CD11b+ cells. The CD20 negative cells that were positive for either CD45 or CD11b or both CD45 and CD11b were collected for microglial/macrophages library preparations.
Post-sorting, isolates were concentrated to approximately 1000 cells per µL, and assessed by trypan blue for viability and concentration. Based on 10× Genomics parameters targeting 8000 cells, the ideal volume of cells was loaded onto the 10× Genomics (Pleasanton, CA, USA) Chromium GEM Chip and placed into the Chromium Controller for cell capturing and library preparation. This occurs through microfluidics and combining with Single Cell 3’ Gel Beads containing unique barcoded primers with a unique molecular identifier (UMI), followed by lysis of cells and barcoded reverse transcription of RNA, amplification of barcoded cDNA, fragmentation of cDNA to 200 bp, 5’ adapter attachment, and sample indexing as the manufacturer instructed with version 3 reagent kits. The prepared libraries were then sequenced using Illumina (San Diego, CA, USA) Nextseq550 and Novaseq6000 sequencers.

treatment_protocol: Three acute-infected rhesus macaques (93T, 94T, and 95T) were intravenously inoculated with SIVmac251

value: Brain

value: CD11b and/or CD45 positive cells


title: PASFIF-R RNA-seq

value: Relapse


title: UM2O

city: Hong Kong

first: Huogang

last: WANG

state: Not Applicable

address: 22 Sassoon Road

department: Obstetrics and Gynecology

institute: The University of Hong Kong

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast  FASTQ preprocessor with useful quality. Clean data (clean reads) were obtained after  quality control, adapter trimming, quality filtering and per-read quality cutting. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Paired-end clean reads were aligned to the reference genome  using HISAT2 v2.1.0 (hierarchical indexing for spliced alignment of transcripts), which  is a highly efficient system for aligning reads from RNA sequencing experiments.  HISAT2 uses an indexing scheme based on the Burrows-Wheeler transform and the  Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole_x0002_genome FM index to anchor each alignment and numerous local FM indexes for very  rapid extensions of these alignments. HISAT2 is the fastest system currently available,   with equal or better accuracy than any other method. HISAT2 was run with the default  parameters.
Featurecount was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with |log2(FoldChange)| > 1 and adjusted P_x0002_value
Genome_build: homo sapiens reference genome (GRCh38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Macrophages were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: macrophage induction

value: monocyte treated with PMA for 24h and refresh medium for 24h to obtain macrophages

tag: m1/m2 polarization

value: IL4/IL13 treat for 48h to obtain M2

value: Incubated with with Omental conditional medium (OCM) for 24h


title: 111T_Micro2,Rhesus Macauqe,control,non-infection


title: Exp#1_Lsd1_RIP_0317


title: PASMEN-R RNA-seq


title: 111T_Micro1,Rhesus Macauqe,control,non-infection


title: C2 offshore to offshore, treatment [high_C2_off]

description:
high_C2_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S31


title: SJPHALL005-R RNA-seq


title: UM2C

value: Incubated with control medium for 24h


title: UM1O

value: LPS/IFN-γ treat for 48h to obtain M1


title: PASFIF-D RNA-seq

value: Diagnosis


title: Sample 10_SF7761, ChIP-seq H2A.Z, SB939

value: brain

value: H3.3K27M mutant


title: C1 offshore to offshore, treatment [high_C1_off]

description:
high_C1_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S33

value: coral tissue


title: 104T_Micro4,Rhesus Macauqe,control,non-infection


title: UM1C


title: SJPHALL005-D RNA-seq


title: 111T_Micro4,Rhesus Macauqe,control,non-infection


title: TM2O


title: B6 inshore to offshore, treatment [high_B6_off]

description:
high_B6_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S52

value: in


title: 104T_Micro3,Rhesus Macauqe,control,non-infection


title: B3 inshore to offshore, treatment [high_B3_off]

description:
high_B3_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S34

value: Offshore


title: SJETV043-R RNA-seq

value: B-ALL


title: brain, Female, Pink1-/-, 548

city: Madison

first: Cynthia

middle: A

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Goblin (alpha and beta) were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used
Supplementary files format and content: tab-delimited text files include raw values for each sample.

organism: Rattus norvegicus

extract_protocol:
Brains were dissected, flash frozen on dry ice, and RNA was harvested using the Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad, Hercules, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: Female

tag: age

value: 8 months


title: TM2C


title: SJETV043-D RNA-seq

value: primary bone marrow


title: B1 inshore to offshore, treatment [high_B1_off]

description:
high_B1_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S55


title: TM1C


title: RNA ArD_0h _1

data_processing:
The original image data were transferred into sequencing data by base calling and generate raw reads.
Clean data including clean reads were obtained by removing the raw reads which contains an adapter, poly-N or with low quality.
Subsequently, Q20, Q30 and GC contents of the clean data were calculated for the quality control.All the downstream analysis was based on the high quality clean data.
Artemia genome from NCBI database was used as the reference genome for genome mapping. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The FPKM of each gene was calculated based on the length and reads count mapped to the gene. FPKM is the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Assembly: Artemia genome from NCBI database
Supplementary files format and content: excel file contains the raw count and fpkm values for each sample

extract_protocol:
The total RNA from Artemia cysts was isolated using TRIzol reagent and treated with RNase-free DNase I to remove any contaminating genomic DNA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina novaseq platform and 150 bp paired-end reads were generated.

value: cyst

value: Artemia parthenogenetica

value: WT

value: no treatment


title: PANGUA-R RNA-seq

value: Relapse


title: V0

city: Changsha

first: Hao

last: Yue

address: No. 892 Yuanda 2nd Road, Mapoling, Furong District, Changsha City, Hunan Province

institute: Hunan university

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We   processed the unique molecular identifier (UMI) count matrix using the R package Seurat (version 3.1.1).
To remove low quality cells and likely multiplet captures,   which is a major concern in microdroplet-based experiments, we applied a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers. Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where >10% of the counts belonged to mitochondrial genes.
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
The most variable genes were selected using FindVariableGenes  function(mean.function = ExpMean, dispersion.function = LogVMR) in Seurat.Principal component analysis (PCA) was performed to reduce the dimensionality with RunPCA function in Seurat. Graph-based clustering was performed to cluster cells according to their gene expression profile using the FindClusters function in Seurat.Cells were visualized using a 2-dimensional t-distributed stochastic neighbor embedding (t-SNE) algorithm with the RunTSNE function in Seurat. We used the FindAllMarkers function(test.use = bimod) in Seurat to identify marker genes of each cluster
Differentially expressed genes(DEGs) were identified using the FindMarkers function(test.use = MAST) in Seurat. P value < 0.05 and |log2foldchange| > 0.58 was set as the threshold for significantly differential expression. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Assembly: Solanum_lycopersicum_v4.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Solanum lycopersicum

source_name: tomato leaf

extract_protocol:
The leaves of tomato plants were cut and immediately transferred into the enzyme solutionnby vacuum infiltration for 30 min.  The samples were then protoplasted for 2 hours at 20℃ on an orbital shaker set at 200 g. Cells were then filtered with a 40 µm cell strainer.The WI solution  was added and shaken vigorously to release the protoplasts. The protoplasts were collected by centrifugation at 200 g, and then washed with the WI solution after which the supernatant was removed by centrifugation. Cell activity was detected by trypan blue staining and cell concentration was measured with a hemocytometer.
The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ Gel Beads-in-emulsion (GEM) Library & Gel Bead Kit v3.

value: leaf

value: 10 days

value: ToCV infection


title: B2 inshore to offshore, treatment [high_B2_off]

description:
high_B2_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S32


title: 104T_Micro1,Rhesus Macauqe,control,non-infection

value: Brain

value: CD11b and/or CD45 positive cells


title: B4 inshore to offshore, treatment [high_B4_off]

description:
high_B4_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S30

value: coral tissue


title: 4SPFC-G-J-101

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description:
E6-1 (ATCC TIB-152)
Crosslinked DNA (HiC)

data_processing:
HiC pipeline including alignment, filtering and postprocessing by the Juicer pipeline, version 1.6.
Filtering of reads below a quality of 30. H5 matrices were generated from .h5 files with HiCExplorer, version 3.6.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: h5 HiC matrices at resolution of 100k bp bins.

source_name: ATCC Jurkat cells

growth_protocol: Grown in RPMI + 10% FCS + Penicillin/Streptomycin, split every second day.

extract_protocol:
Crosslinked with 3% Formaldehyde-PBS, quenched with 1.1M Glycin (final concentration) after 3 minutes. Washed cell pellets with PBS. Subsequent HiC protocol steps were performed with the commercial ArimaKit HiC.
Commercial Arima-HiC library.

value: Jurkat T cells

tag: condition

value: GC


title: TM1O

value: monocyte treated with PMA for 24h and refresh medium for 24h to obtain macrophages

value: LPS/IFN-γ treat for 48h to obtain M1

value: Incubated with with Omental conditional medium (OCM) for 24h


title: PANGUA-D RNA-seq

value: B-ALL

value: primary bone marrow

value: Diagnosis


title: A6 inshore to offshore, treatment [high_A6_off]

description:
high_A6_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S44

value: in

value: Offshore


title: V2

value: 40 days


title: V1

value: leaf

value: 30 days


title: 104T_Micro2,Rhesus Macauqe,control,non-infection


title: C6 offshore to offshore, control [cont_C6_off]

description:
cont_C6_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S43

value: off


title: A5 inshore to offshore, treatment [high_A5_off]

description:
high_A5_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S41


title: SJINF001-D RNA-seq


title: PASYFN-R RNA-seq

value: Relapse


title: SJINF001-R RNA-seq


title: A3 inshore to offshore, treatment [high_A3_off]

description:
high_A3_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S39


title: IRF1KO_M238_6h-IFNG, mRNA-Seq, clone2

city: los angeles

first: Prabhat

middle: Kumar

last: Purbey

state: California

address: 675 Charles E. Young Drive South

department: MIMG

institute: UCLA

data_processing:
RNA-seq libraries were sequenced, single end 50bp on an Illumina HiSeq 3000.
RNA-seq fastq files were mapped using Hisat2. Only the uniquely mapped reads were kept for further analysis.
Uniquely aligned reads were used to quantify against exon in seqmonk to generated read counts matrix
Bedgraph files were generated using Bedtools
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample was generated using Bedtools (genomeCoverageBed)

molecule: polyA RNA

growth_protocol: MC38 cell line was maintained in DMEM with 10% fetal bovine serum, 2mM L- glutamine (Gibco, #25030-081), 0.1 mM non-essential amino acids (Gibco, #11140-050), 1 mM sodium pyruvate (Gibco, #11360-070), 10 mM Hepes (Gibco, #15630-080), and 1X pen/strep (Gibco, #15140-122). YUMM2.1, B16F10  and M238 cell lines were maintained in DMEM with 10% fetal bovine serum.

extract_protocol:
RNAeasy plus kit was used to prepare RNA and 500ng of total RNA was used to generate stranded libraries using TruSeq Stranded mRNA Sample Prep Kit from Illumina.
libraries were constructed using Illumina TruSeq Stranded mRNA Sample Prep Kit according to manufactuer's instruction.

treatment_protocol: IFN-y (Peprotech #315-05) at a concentration 100 units per milli liter was used to stimulate WT or Irf1-/- MC38 cells for 2h in small 3.5 cm plate. Human IFN-y (Invivogen,  Cat# rcyec-hifng) at a concentration 100 units per milli liter was used to stimulate WT or Irf1-/- M238 cells (human melanoma) for 6h in small 3.5 cm plate.

value: human Melanoma

value: IFN-y for 6h


title: T-cells allo-HSCT, d+106 ex vivo, 8-OHdG low, 3 [KMT65d106]

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

country: Germany

institute: Biozentrum

description: samples ex vivo allo-HSCT patients - no treatment ex vivo

data_processing:
Adapters were clipped by trim_galore
Sequence reads were mapped by STAR aligner
Counting with featureCounts
Analysed using edgeR, normallized with TMM method
Supplementary files format and content: GRCh38
Supplementary files format and content: Tab-delimited normalized cpm

source_name: peripheral blood

extract_protocol:
RNA was extracted using  the innuPREP DNA/RNA Mini Kit (Analytik Jena AG, Jena, Germany); on column DNAse digestion was used to remove genomic DNA contamination (RNAse-Free DNase Set, Qiagen, Venlo, Netherlands). RNA was diluted in RNase free H2O to a maximum concentration of 200 ng/μl.
INVIEW transcriptome Explore (Eurofins)

value: low oxidative DNA damage

value: peripheral blood

value: primary T-cells

value: Allogeneic hematopoietic stem cell transplantation (allo-HSCT)


title: 4SPFC-G-J-097

value: Jurkat T cells

value: GC


title: 4SPFC-F-J-093


title: PASYFN-D RNA-seq

value: B-ALL

value: primary bone marrow


title: C4 offshore to offshore, control [cont_C4_off]

description:
cont_C4_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S51

value: coral tissue


title: 4SPFC-F-J-091


title: WT_M238_6h-IFNG, mRNA-Seq, clone2

value: WT

value: untreated


title: PASJTK-R RNA-seq


title: C5 offshore to offshore, control [cont_C5_off]

description:
cont_C5_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S54

value: Offshore


title: 4SPFC-G-J-099


title: C3 offshore to offshore, control [cont_C3_off]

description:
cont_C3_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S24


title: WT_M238_6h-IFNG, mRNA-Seq, clone1


title: H

value: leaf

value: 30 days

value: normal growth


title: IRF1KO_M238_6h-IFNG, mRNA-Seq, clone1

value: human Melanoma


title: 4SPFC-F-J-087

value: hypg


title: PATSAH-D RNA-seq

value: Diagnosis


title: C2 offshore to offshore, control [cont_C2_off]

description:
cont_C2_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S3

value: off


title: 4SPFC-F-J-086


title: C1 offshore to offshore, control [cont_C1_off]

description:
cont_C1_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S5


title: PATSAH-R RNA-seq

value: Relapse


title: B6 inshore to offshore, control [cont_B6_off]

description:
cont_B6_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S13

value: in


title: 4SPFC-F-J-085

value: Jurkat T cells


title: PASJTK-D RNA-seq


title: IRF1KO_M238,untreated, mRNA-Seq, clone2

value: IFN-y for 6h


title: PATJJX-D RNA-seq

value: B-ALL


title: B4 inshore to offshore, control [cont_B4_off]

description:
cont_B4_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S21


title: PATJJX-R RNA-seq

value: primary bone marrow


title: 4SPFC-F-J-083

value: 1g IF


title: WT_M238, untreated, mRNA-Seq, clone1

value: WT


title: WT_M238, untreated, mRNA-Seq, clone2

value: untreated


title: 4SPFC-F-J-089


title: 4SPFC-F-J-082


title: B3 inshore to offshore, control [cont_B3_off]

description:
cont_B3_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S40

value: coral tissue

value: Offshore


title: Wild Type 5

city: Morgantown

first: David

middle: Rodrigo

last: Salcedo

state: WV

address: 64 Medical Center Drive

department: Biochemistry and Molecular Medicine

institute: West Virginia University

data_processing:
Quality Check FASTQC
Aligment with HISAT2.0
Counts quantify featureCounts
Filtering 0 and NA constant values
Normalization with DESEQ2.0 and differential expression analysis
Assembly: WS245
Supplementary files format and content: Normalized reads FPKM

organism: Caenorhabditis elegans

source_name: Wild type

growth_protocol: Worms were mantained in NGM plates at 20C feeded with OP50

extract_protocol:
Total RNA was extracted with TRIZOL according to protocols by the manufacter
mRNA library preparation (poly A enrichment)

treatment_protocol: No treatment

value: day 8

value: Wild type


title: B2 inshore to offshore, control [cont_B2_off]

description:
cont_B2_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S22


title: PATIKJ-R RNA-seq


title: Wild Type 4


title: PATIKJ-D RNA-seq


title: B1 inshore to offshore, control [cont_B1_off]

description:
cont_B1_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S53


title: Wild Type 3


title: PASPNY-R Hi-C

data_processing:
hic-bench platform
Reads filtered for accepted intra-chromosomal read-pairs by the GenomicTools tools-hic filter command in the hic-bench platform
Interaction matrices for each chromosome separately were created by the hic-bench platform at 40kb resolution
Filtered read counts were normalized by iterative correction and eigenvector decomposition
To account for variances in read counts of more distant loci, distance normalization for each chromosome matrix was performed.
Assembly: hg19
Supplementary files format and content: .hic files consisting of hic signal and compartment bedgraphs consisting of A/B compartment tracks for each patient

extract_protocol:
Following FACS, leukemic cells were immediately fixed and crosslinked with 2% formaldehyde at room temperature for 10 minutes. Glycine was added to stop the reaction. Crosslinked cells were washed with PBS and then frozen on dry ice. Crosslinked cell pellets were stored at -80 until ready for processing.
Hi-C libraries were generated using the Arima-HiC kit (A410110) with Swift Biosciences® Accel-NGS® 2S Plus DNA Library Kit (Cat # 21024) and Indexing kit (Cat #) according to manufacturer’s protocol.


title: IRF1KO_M238,untreated, mRNA-Seq, clone1

value: human Melanoma


title: A6 inshore to offshore, control [cont_A6_off]

description:
cont_A6_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S14


title: A5 inshore to offshore, control [cont_A5_off]

description:
cont_A5_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S6


title: Wild Type 1


title: PASMEN-R Hi-C


title: A3 inshore to offshore, control [cont_A3_off]

description:
cont_A3_off
kallisto.isoform.counts.matrix_trenchii.txt
5286-S4


title: Wild Type 2


title: C6 offshore to inshore, treatment [high_C6_in]

description:
high_C6_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S27

value: Inshore


title: PASMEN-D Hi-C

value: Diagnosis


title: Hyperactive Mutant 4

source_name: α3ΔN deletion of pas-3

value: hyperactive proteasome mutant


title: 4SPFC-F-J-081

description:
E6-1 (ATCC TIB-152)
Crosslinked DNA (HiC)


title: PASFIF-D Hi-C


title: R after  3

type: RNA

city: Seoul

first: Kelun

last: Zhang

state: Seoul

address: 50-1, Yonsei-Ro, Seodaemun-gu

department: Dermatology

country: South Korea

institute: Yonsei university

description:
Peripheral blood mononuclear cell-derived CD4+CD25hiCD127low cells in SIT responsive (R) AD patients after immunotherpy
Human PBMC for Allergen immunotherpy

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC). R 4.1.2 (www.r-project.org) and Bioinformatics tool (www.bioinformatics.com) were employed for all data analysis and visualization of differentially expressed genes, and the comparative analysis
log2 FC

label: biotin

source_name: After treatment in the Allergen-specific immunotherapy effective response group

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: For transcriptome analysis, peripheral blood samples were collected from patients who had received 12 months of specific immunotherapy (SIT) using an HDM allergen extract or placebo.

extract_protocol: PBMCs were isolated through density centrifugation on a Ficoll-Paque™ plus (Amersham Biosciences). Treg cells were sorted with a FACSAria III (BD Biosciences) using the CD3+CD4+CD25high CD127low strategy

treatment_protocol: Peripheral blood samples were obtained from patients with AD exhibiting positive responses to SIT (R, n=3) and those who did not show improvement with SIT (Non-R, n=3). Blood samples were collected before and after administering SIT.

tag: human pbmc

value: peripheral blood mononuclear cells

tag: responsive or non-respnsive sit

value: Respnsive

tag: before and after sit

value: After


title: C5 offshore to inshore, treatment [high_C5_in]

description:
high_C5_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S38

tag: tissue

value: off


title: PASFIF-R Hi-C

tag: disease state

value: B-ALL

tag: cell type

value: Relapse


title: R before  3

description:
Peripheral blood mononuclear cell-derived CD4+CD25hiCD127low cells in SIT responsive (R) AD patients before immunotherpy
Human PBMC for Allergen immunotherpy

source_name: Before treatment in the Allergen-specific immunotherapy effective response group

value: Before


title: R after  2


title: R after  1


title: Hyperactive Mutant 3

tag: genotype


title: SJPHALL005-R Hi-C

value: primary bone marrow


title: R before  1


title: PASPNY-D Hi-C


title: C4 offshore to inshore, treatment [high_C4_in]

description:
high_C4_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S17

tag: treatment


title: SJPHALL005-D Hi-C


title: C3 offshore to inshore, treatment [high_C310_in]

description:
high_C310_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S49


title: T-cells allo-HSCT, d+90 ex vivo, 8-OHdG high, 2 [KMT138d90]

description: samples ex vivo allo-HSCT patients - no treatment ex vivo

value: high oxidative DNA damage

value: peripheral blood

value: primary T-cells

value: Allogeneic hematopoietic stem cell transplantation (allo-HSCT)


title: Hyperactive Mutant 1

value: day 8


title: C2 offshore to inshore, treatment [high_C2_in]

description:
high_C2_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S35

value: coral tissue


title: B2_AGY1863_Gen0_Rep3

first: Audrey

last: Gasch

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

description:
1863_time0_rep3
Batch2_Dutcher_barcode_cts.csv

library_source: other

data_processing:
library strategy: BAR-seq
Read counts generated using a script to identify samples from fastq files that are associated with each 10bp index tag
Assembly: YPS1009
Supplementary files format and content: Raw Count data, csv files

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Strains used in the study are all haploids of the YPS1009 background. 1 mL frozen glycerol stocks of librarytransformed cells were thawed into 100 mL of liquid SC-His with nourseothrycin (NTC, 100 mg/L) to ensure maintenance of amplified chromosomes and G418 (200 mg/L) to maintain plasmids at a starting OD600of 0.05, then grown in shake flasks at 30°C with shaking. The remaining cells from the frozen stocks were pelleted by centrifugation and represented the starting pool (generation 0) for each strain. After five generations, each pooled culture was diluted to an OD600of 0.05 in fresh media, in order to maintain cells in log phase. At 10 generations (and 5 generations for a subset of strains), cells were harvested and cell pellets were stored at −80°C.

extract_protocol:
Plasmids were recovered from each pool using Zymoprep Yeast Plasmid Miniprep II (Zymo Research D2004-A) with the following modifications: samples were incubated with 15 units zymolyase at 37°C for 1 hour, with inversion every 15 minutes; incubation in cell lysis buffer was extended to 10 minutes; after neutralization, samples were put on ice for 30 minutes, then centrifuged at 4°C.
Plasmid barcodes were amplified using primers containing Illumina multiplex adaptors as described in (Piotrowski et al. 2015), with number of PCR cycles reduced to 20. Barcode amplicons were pooled and purified using AxyPrep Mag beads (1.8X volume beads per sample volume) according to the manufacturer’s instructions (Axygen).

tag: strain

tag: genetic lineage

value: North American

tag: generation

tag: media

tag: molecule type

value: plasmid DNA


title: Hyperactive Mutant 5

value: hyperactive proteasome mutant


title: B2_AGY1863_Gen0_Rep2

description:
1863_time0_rep2
Batch2_Dutcher_barcode_cts.csv


title: SJETV043-D Hi-C

value: Diagnosis


title: NR after  3

description:
Peripheral blood mononuclear cell-derived CD4+CD25hiCD127low cells in SIT non-responsive (Non-R) AD patients after immunotherpy
Human PBMC for Allergen immunotherpy

source_name: After treatment in the Allergen-specific immunotherapy Non-response group

value: peripheral blood mononuclear cells

value: Non-Respnsive


title: C1 offshore to inshore, treatment [high_C1_in]

description:
high_C1_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S46

tag: origin

value: off

tag: transplant

value: Inshore

tag: collection site


title: B2_AGY1863_Gen0_Rep1

description:
1863_time0_rep1
Batch2_Dutcher_barcode_cts.csv


title: R before  2

value: Respnsive


title: Hyperactive Mutant 2

tag: age


title: B4 inshore to inshore, treatment [high_B4_in]

description:
high_B4_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S37

value: in


title: B2_AGY1863_Gen10_Rep3

description:
1863_10gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: PANGUA-D Hi-C

value: B-ALL

value: primary bone marrow


title: Plasmid

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

description: Plasmid DNA

data_processing:
Illumina binary base call (BCL) files were converted into fastq file format by Illumina bcl2fastq software (v. 2.17).
Paired reads were merged using Pear (v. 0.9.11), and trimmed using cutadapt (v. 2.8).
The trimmed reads were mapped to the human GeCKOv2 library by Bowtie (v. 1.2.3).
The sgRNA count matrix was obtained from Bowtie output sam files.
Data from each sample were merged into a single table of unfiltered counts with R software (v. 4.2.2).
Assembly: Human Genome-Scale CRISPR Knock-Out (GeCKO) lentiviral pooled library (GeCKO v2, library A, cat. 1000000048, Addgene)
Supplementary files format and content: Tab delimited file containing the unfiltered counts from Bowtie alignment

organism: Escherichia coli

source_name: Plasmid library after amplification of Human Genome-Scale CRISPR Knock-Out (GeCKO) lentiviral pooled library (GeCKO v2, library A, cat. 1000000048, Addgene)

growth_protocol: HFF were maintained in Dulbecco's modified Eagle Medium (DMEM, cat. 11965, ThermoScientific) supplemented with 15% fetal bovine serum (FBS, ThermoScientific) at 37°C and 5% CO2. Cells were maintained on culture-ware (including transwells) coated with Matrigel growth factor reduced (MGFR, 50 μg/mL overnight at 4°C and 1 h at 37°C, cat. 354230, Corning) and passaged by 0.25% trypsin digestion (ThermoScientific) before reaching confluency.

extract_protocol:
Genomic DNA was extracted using Quick-gDNA MidiPrep (Zymo Research) following manufacturer's instructions
Genomic DNA amplification for Next Generation Sequencing analysis was performed according to Joung et al. (10.1038/nprot.2017.016)
Library preparation for Next Generation Sequencing analysis was performed according to Joung et al. (10.1038/nprot.2017.016)

treatment_protocol: Cells were transduced with the Human Genome-Scale CRISPR Knock-Out (GeCKO) lentiviral pooled library (GeCKO v2, library A, cat. 1000000048, Addgene), and cultured either in standard flasks or in transwell devices.

tag: cell line

value: Library amplification was performed as in Joung et al. (10.1038/nprot.2017.016)


title: NR after  2

tag: human pbmc

tag: responsive or non-respnsive sit

value: After


title: NR before  2

description:
Peripheral blood mononuclear cell-derived CD4+CD25hiCD127low cells in SIT non-responsive (Non-R) AD patients before immunotherpy
Human PBMC for Allergen immunotherpy

source_name: Before treatment in the Allergen-specific immunotherapy Non-response group

tag: before and after sit

value: Before


title: NR after  1


title: SJINF001-R Hi-C

tag: disease state

value: Relapse


title: B2_AGY1863_Gen10_Rep2

description:
1863_10gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: NR before  3


title: B3 inshore to inshore, treatment [high_B3_in]

description:
high_B3_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S19

tag: tissue

value: coral tissue


title: SJETV043-R Hi-C

tag: cell type

tag: genotype


title: B2 inshore to inshore, treatment [high_B2_in]

description:
high_B2_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S28

tag: treatment


title: SJINF001-D Hi-C


title: NR before  1


title: B2_AGY1863_Gen10_Rep1

description:
1863_10gen_rep1
Batch2_Dutcher_barcode_cts.csv

tag: strain

tag: genetic lineage

value: North American


title: PANGUA-R Hi-C


title: B6 inshore to inshore, treatment [high_B6_in]

description:
high_B6_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S26


title: PASYFN-R Hi-C


title: B1 inshore to inshore, treatment [high_B1_in]

description:
high_B1_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S25


title: B2_AGY1862_Gen0_Rep3

description:
1862_time0_rep3
Batch2_Dutcher_barcode_cts.csv

tag: generation

tag: media

value: plasmid DNA


title: DT 72h B rep2

city: Houston

first: Jason

middle: C

last: Mills

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Labelled cDNA hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays according to manufacturers instructions and placed in GeneChip Hybridization Oven 620 for 18hr at 45C. Microarrays were washes and stained with Affymettrix Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip® 7G Scanner 3000 laser confocal slide scanner

data_processing: Microarray data data expression was process using Command Console (Affymetrix, Inc) and the raw .CEL files were analyzed using Partek Genomic Suite v7.0 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

label: Biotin

organism: Mus musculus

source_name: Diphtheria-Toxin treated+ 72h recovery

label_protocol: Total RNA was extracted and used to prepare biotinylated cDNA with Affymetrix WT plus reagent kit

growth_protocol: Mice were grown in a temperature and light controlled mouse facility; littermate controls were used when possible. Adult mice age 8-12 weeks were used.

extract_protocol: Total RNA extracted, purified by RNEasy Micro Kit, and RNA intergrity verified on Agilent Bioanalyzer

treatment_protocol: Diphtheria toxin (225ng/mouse) or saline vehicle was administered via ip injuection daily for three days. Mice were euthanized at 24, 36, 48, or 72 hours after final siphtheria toxin injection

value: Gastric Corpus Tissue


title: PASJTK-R Hi-C

first: Sonali

last: Narang

institute: NYU Langone

source_name: primary bone marrow


title: A6 inshore to inshore, treatment [high_A6_in]

description:
high_A6_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S47

tag: origin


title: PASYFN-D Hi-C

value: Diagnosis


title: B2_AGY1862_Gen0_Rep2

description:
1862_time0_rep2
Batch2_Dutcher_barcode_cts.csv

tag: molecule type


title: A5 inshore to inshore, treatment [high_A5_in]

description:
high_A5_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S18

tag: transplant

tag: collection site


title: B2_AGY1862_Gen0_Rep1

description:
1862_time0_rep1
Batch2_Dutcher_barcode_cts.csv


title: A3 inshore to inshore, treatment [high_A3_in]

description:
high_A3_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S29


title: B2_AGY1862_Gen10_Rep2

description:
1862_10gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: C6 offshore to inshore, control [cont_C6_in]

description:
cont_C6_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S12


title: DT 72h A rep1


title: PASJTK-D Hi-C


title: PATSAH-D Hi-C


title: PATSAH-R Hi-C


title: C5 offshore to inshore, control [cont_C5_in]

description:
cont_C5_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S8


title: B2_AGY1862_Gen10_Rep1

description:
1862_10gen_rep1
Batch2_Dutcher_barcode_cts.csv


title: B2_AGY1861_Gen0_Rep3

description:
1861_time0_rep3
Batch2_Dutcher_barcode_cts.csv


title: PATJJX-R Hi-C


title: PATJJX-D Hi-C


title: C3 offshore to inshore, control [cont_C34_in]

description:
cont_C34_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S1


title: C4 offshore to inshore, control [cont_C4_in]

description:
cont_C4_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S7


title: B2_AGY1861_Gen0_Rep2

description:
1861_time0_rep2
Batch2_Dutcher_barcode_cts.csv


title: B2_AGY1862_Gen10_Rep3

description:
1862_10gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: DT 36h

source_name: Diphtheria-Toxin treated+ 36h recovery


title: PATIKJ-R Hi-C


title: B2_AGY1861_Gen0_Rep1

description:
1861_time0_rep1
Batch2_Dutcher_barcode_cts.csv


title: C2 offshore to inshore, control [cont_C2_in]

description:
cont_C2_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S50


title: B2_AGY1861_Gen5_Rep3

description:
1861_5gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: C1 offshore to inshore, control [cont_C1_in]

description:
cont_C1_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S11


title: PATIKJ-D Hi-C


title: SJPHALL005-R ATAC

data_processing:
Slide-n-Seq (sns) pipeline: https://igordot.github.io/sns/
Aigned to reference genome (hg19) using Bowtie2
Filtering of duplicate reads by Sambamba
Peak-calling conducted with MACS2
Assembly: hg19
Supplementary files format and content: bigwigs and bedfiles with MACS2 peak calls for each sample

extract_protocol:
Following FACS, 50,000 leukemic cells were immediately processed for ATACseq by the NYU Genome Technology Center.
ATAC libraries were generated based on the protocol by Buenrostro et al. Briefly, cells are resuspended in cold lysis buffer (10 mM Tris Cl, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630, pH 7.4) and centrifuged for 1 minuted at 500xg. with one modification. Nuclei were tagmented using Nextera (Illumina) Tagmentation DNA buffer and enzyme.


title: B2_AGY1861_Gen5_Rep2

description:
1861_5gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: DT 48h rep1

source_name: Diphtheria-Toxin treated+ 48h recovery


title: B6 inshore to inshore, control [cont_B6_in]

description:
cont_B6_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S16


title: B4 inshore to inshore, control [cont_B4_in]

description:
cont_B4_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S15


title: SJETV043-R ATAC


title: B2_AGY1861_Gen5_Rep1

description:
1861_5gen_rep1
Batch2_Dutcher_barcode_cts.csv


title: PANGUA-R ATAC


title: B3 inshore to inshore, control [cont_B3_in]

description:
cont_B3_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S36


title: B2 inshore to inshore, control [cont_B2_in]

description:
cont_B2_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S10


title: DT 48h rep2


title: SJINF001-R ATAC


title: B2_AGY1860_Gen0_Rep2

description:
1860_time0_rep2
Batch2_Dutcher_barcode_cts.csv


title: PASPNY-R ATAC


title: Uninjured Control

source_name: Vehicle treated


title: CD8 T cells, chronic HCV advanced fibrosis, pre-DAA, participant 171

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Processed raw sequences with fastp to perform automatic adapter trimming, and default sequence quality filtering (>60% of bases with Q≥15, and no more than 5 'N' basecalls)
Quantified transcripts from GENCODE v29 with salmon v0.11.3 using --gcBias flag
Performed fold change analysis using DESeq2 as follows
Read transcript quantification data with tximport library and summarized to gene level quantification
Filtered to retain genes with at least 5 reads assigned in at least two samples
Constructed DESeqDataSet object with twelve samples using the model ~condition (treatment) or ~condition + patient
Calculated fold changes using the results() function, then ran lfcShrink() on the results using the apeglm method.
Assembly: GRCh38
Supplementary files format and content: salmon transcript quantification: Quantifrication of GENCODE v29 transcripts using salmon v0.11.3

source_name: CD8 T cells

growth_protocol: CD8 T cells isolated from cryopreserved PBMCs were cultured in RPMI 1640 supplemented with 20% FBS.

extract_protocol:
Total RNA was isolated using TRIzol Reagent following manufacturer's protocol.
Libraries were generated using the TruSeq RNA/DNA Library Preparation Kit.

treatment_protocol: CD8 T cells were stimulated with 0.5 µg/ml phytohemaglutanin-L for 18h prior to total RNA extraction.

value: CD8 T cells


title: B1 inshore to inshore, control [cont_B1_in]

description:
cont_B1_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S48

data_processing:
Adapters and low-quality reads were removed in Trimmomatic v0.36 (phred33, quality score > 20, 4 bp sliding window; Bolger, Lohse, and Usadel 2014)
The metatranscriptome was filtered by performing BLASTx (e-value < 1e−5) searches against two coral proteomes, and BLASTn (e-value < 1e−5) searches against four Symbiodiniaceae genomes (as of June, 2018) (coral: Acropora digifitera and Orbicella faveolata. Symbiodiniaceae: Symbiodinium microadriaticum; Breviolum minutum; Cladocopium goreaui; Durusdinium trenchii).
Trinity scripts (Grabherr et al., 2011) were used to map the reads back to both transcriptomes using the alignment-based abundance estimation method RSEM (RNA-Seq by Expectation-Maximization) and to build an expression matrix from the transcript abundance files.
Assembly: Trinity scripts (Grabherr et al., 2011)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: coral tissue

extract_protocol:
Total RNA was extracted using the total RNAqueous kit (AM1912, Life Technologies), according to the manufacturer’s instructions
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit following the manufacturer’s protocol at the Duke Center for Genomic and Computational Biology


title: B2_AGY1860_Gen0_Rep1

description:
1860_time0_rep1
Batch2_Dutcher_barcode_cts.csv


title: A6 inshore to inshore, control [cont_A6_in]

description:
cont_A6_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S2


title: PASPNY-D ATAC

city: New York

address: 435 east 30th street


title: GBM8401_DMSO CTRL_48hr_rep1

city: Taipei

first: Yung Lung

last: Chang

address: Rm. 7309, 7F., No.161, Sec. 6, Minquan E. Rd., Neihu Dist.

department: Biochemistry

institute: National Defense Medical Center

hyb_protocol: HOA v7.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 microg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by limma package (Bioconductor). The control probes were filtered out and then normalized by the median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by empirical bayes statistics and presented by log2 ratio and p-value.

label_protocol: The 1 microg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Both cells were grown in DMEM medium with 2% FBS.

extract_protocol: Total RNA was extracted using Trizol according to manufacturer's protocol.

treatment_protocol: Cells were seeded in 6-well plates and then incubated overnight to allow cells to attach. Cells were harvested after the treatment of 10 microM Momordicine or DMSO control for 48 hrs.

value: Vehicle control


title: CD8 T cells, chronic HCV minimal fibrosis, 24W post-SVR, participant 137


title: GBM8401_Momordicine_10microM_48hr_rep2

value: Momordicine 10 microM


title: DT 24h

source_name: Diphtheria-Toxin treated+ 24h recovery


title: CD8 T cells, chronic HCV minimal fibrosis, pre-DAA, participant 137


title: GBM8401_DMSO CTRL_48hr_rep2


title: A5 inshore to inshore, control [cont_A5_in]

description:
cont_A5_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S9

value: Inshore


title: LN229_Momordicine_10microM_48hr_rep1


title: CD8 T cells, chronic HCV advanced fibrosis, pre-DAA, participant 136


title: LN229_DMSO CTRL_48hr_rep2


title: A3 inshore to inshore, control [cont_A3_in]

description:
cont_A3_in
kallisto.isoform.counts.matrix_trenchii.txt
5286-S45


title: GBM8401_Momordicine_10microM_48hr_rep1


title: LN229_Momordicine_10microM_48hr_rep2


title: CD8 T cells, chronic HCV advanced fibrosis, 24W post-SVR, participant 133


title: B2_AGY1860_Gen0_Rep3

description:
1860_time0_rep3
Batch2_Dutcher_barcode_cts.csv


title: B2_AGY1860_Gen5_Rep1

description:
1860_5gen_rep1
Batch2_Dutcher_barcode_cts.csv


title: PATIKJ-D ATAC


title: LN229_DMSO CTRL_48hr_rep1


title: PASYFN-R ATAC


title: Brz treated Col-0_rep3

city: Jinan

first: Fengning

last: Xiang

state: Shandong

address: 27, Shandanan Road

department: School of life science

institute: Shandong University

data_processing:
We define "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before
downstream analysis to decrease data noise.Filtering steps are as follows:1) Remove reads with adaptors;
2) Remove reads in which unknown bases are more than 10%;
3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no
more than 5).
After filtering, the remaining reads are called "clean reads" and stored as FASTQ format
In general, the higher ratio of alignment, indicating that the closer the genetic relationship between sample and reference species. The lower rate may be due to low similarity with reference species or there are other pollutions.
We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome. Their alignment parameters change a little according different sequencing strategy (PE or SE):
Bowtie2 parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p
16 -k 200 Bowtie2 parameters for SE reads: -q --phred64 --sensitive --dpad 0 --gbar
99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
HISAT parameters for PE reads: -p 8 --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
HISTA parameters for SE reads: -p 8 --phred64 --sensitive -I 1 -X 1000
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: The seeds were treated at 4 ºC for 4 days and then germinated at 22 ºC under a 16-h light/8-h dark cycle.

extract_protocol:
Total RNA was extracted from 5-day-old light-grown seedlings (Col-0, MIR394A OE and Brz treated Col-0) using the RNeasy Plant Mini kit (Qiagen) according to the manufacturer’s instructions.
The mRNA sequencing libraries were constructed with barcodes using the TrueSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: 2μM Brz was added to the half strength MS medium

value: whole seedlings

tag: age


title: B2_AGY1860_Gen10_Rep3

description:
1860_10gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: CD8 T cells, chronic HCV advanced fibrosis, pre-DAA, participant 133


title: PASYFN-D ATAC


title: B2_AGY1860_Gen5_Rep3

description:
1860_5gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: Brz treated Col-0_rep2


title: PATIKJ-R ATAC


title: PASJTK-R ATAC


title: CD8 T cells, chronic HCV minimal fibrosis, 24W post-SVR, participant 124


title: B2_AGY1860_Gen10_Rep2

description:
1860_10gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: MIR394OE_rep3


title: CD8 T cells, chronic HCV advanced fibrosis, pre-DAA, participant 130


title: B2_AGY1860_Gen10_Rep1

description:
1860_10gen_rep1
Batch2_Dutcher_barcode_cts.csv


title: CD8 T cells, chronic HCV minimal fibrosis, 24W post-SVR, participant 117


title: Brz treated Col-0_rep1


title: B2_AGY1859_Gen0_Rep3

description:
1859_time0_rep3
Batch2_Dutcher_barcode_cts.csv


title: PASJTK-D ATAC


title: MIR394OE_rep2


title: B2_AGY1859_Gen0_Rep2

description:
1859_time0_rep2
Batch2_Dutcher_barcode_cts.csv


title: PASMEN-D ATAC


title: CD8 T cells, chronic HCV minimal fibrosis, pre-DAA, participant 117


title: PASMEN-R ATAC


title: B2_AGY1859_Gen0_Rep1

description:
1859_time0_rep1
Batch2_Dutcher_barcode_cts.csv


title: CD8 T cells, chronic HCV minimal fibrosis, 24W post-SVR, participant 116


title: MIR394OE_rep1


title: Col-0_rep3


title: PASFIF-R ATAC


title: B2_AGY1859_Gen10_Rep3

description:
1859_10gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: CD8 T cells, chronic HCV minimal fibrosis, pre-DAA, participant 116


title: Col-0_rep2


title: B2_AGY1859_Gen10_Rep2

description:
1859_10gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: PASFIF-D ATAC


title: IGFBP63

city: Hefei

first: Meiming

last: Su

address: Huangshan Road

institute: USTC

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM(v1.2.12).
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: endothelium

growth_protocol: Cells were cultured in M200 media supplemented with 5% FBS and 1X ECGS

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen.
RNA libraries were prepared for sequencing using rRNA Removal Library Construction Protocol.

treatment_protocol: HUVECs were treated with AdNC or Ad-IGFBP6 for 24 hours and with or without TNF-α (10ng/ml) for 6 hours.

value: endothelium

value: Human Umbilical Vein Endothelial Cells

value: WT


title: SJPHALL005-D ATAC

value: B-ALL

value: primary bone marrow


title: Mock2-TCR

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: 10x Genomics

data_processing:
Cell Ranger (10x Genomics) functions mkfastq and count were used to align to the bosTau9 genome and demultiplex the sequencing data and generate gene-barcode matrices.
Assembly: bosTau9
Supplementary files format and content: Cell ranger output files
Library strategy: TCR-seq

organism: Bos taurus

source_name: CD8+ T cells

extract_protocol:
CD8+ T lymphocytes filtered through a 40 μm cell strainer and the concentration adjusted to 1200 cells/μL before single cell capture using the Chromium controller (10x Genomics)
Cells were loaded on the Chromium Controller (10x Genomics) and Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5ʹ v1 Reagent Kit (10x Genomics) according to manufacturer’s protocol.

value: CD8+ T cells

value: Non-infected Bovine Turbinates cells


title: IGFBP62


title: B2_AGY1859_Gen10_Rep1

description:
1859_10gen_rep1
Batch2_Dutcher_barcode_cts.csv


title: PANGUA-D ATAC


title: Col-0_rep1


title: B2_AGY1860_Gen5_Rep2

description:
1860_5gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: WT718-TCR

description: 10x Genomics

value: Bovine Turbinates Cells infected with WT strain of AlHV-1


title: SJINF001-D ATAC


title: SJETV043-D ATAC


title: WT718-GEX

description: 10x Genomics

data_processing:
Cell Ranger (10x Genomics) functions mkfastq and count were used to align to the bosTau9 genome and demultiplex the sequencing data and generate gene-barcode matrices.
Assembly: bosTau9
Supplementary files format and content: Cell ranger output files


title: B2_AGY1613_Gen0_Rep2

description:
1613_time0_rep2
Batch2_Dutcher_barcode_cts.csv

value: North American


title: IGFBP61


title: B2_AGY1613_Gen0_Rep1

description:
1613_time0_rep1
Batch2_Dutcher_barcode_cts.csv

value: plasmid DNA


title: B2_AGY1613_Gen5_Rep3

description:
1613_5gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: WT-10

data_processing:
Paired-end reads were mapped to mouse genome bosTau9 with Bowtie2 using default parameters for paired-end reads. Reads that mapped several regions, or with insufficient mapping quality, were removed with samtools view. Duplicate reads were removed with MarkDuplicates tools (Picard suite). Peaks were called with MACS2
Assembly: bosTau9
Supplementary files format and content: bigwig files

source_name: CD8+ T Cells

value: CD8+ T Cells


title: WT-12


title: PATJJX-R ATAC

value: Relapse


title: PATJJX-D ATAC

value: Diagnosis


title: B2_AGY1613_Gen5_Rep2

description:
1613_5gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: TNFa2

value: Ad-NC+TNFa


title: WT-1


title: TNFa1


title: WT-13


title: B2_AGY1613_Gen0_Rep3

description:
1613_time0_rep3
Batch2_Dutcher_barcode_cts.csv


title: PATSAH-D ATAC


title: Contorl3

value: Ad-NC


title: Contorl2


title: Del73-2

value: Bovine Turbinates Cells infected with ORF73-deficient strain of AlHV-1


title: PATSAH-R ATAC


title: B2_AGY1613_Gen10_Rep2

description:
1613_10gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: Del73-1


title: Contorl1


title: B2_AGY1613_Gen10_Rep3

description:
1613_10gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: B2_AGY1613_Gen10_Rep1

description:
1613_10gen_rep1
Batch2_Dutcher_barcode_cts.csv


title: NP35

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

data_processing:
Trimmed sequence reads were mapped to Genome Reference Consortium Human Build 38 (GRCh38)
Counts per millions were log transformed and Trimmed mean of M values normalization was applied to adjust for variation in library size.
Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) and Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) were used for assembly of reads and alignment of the contigs to the human genome assembly
Assembly: GRch38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: renal tissue, FFPE

extract_protocol:
RNA extraction was performed using the miRNeasy FFPE kit (cat. no. 217504; Qiagen, Venlo, The Netherlands), as described previously (13). Following RNA extraction, the samples were stored at -80oC until further use.
RNA library preparation and sequencing were carried out at Functional Genomics Centre Zurich (University of Zurich, Switzerland). The quantity and quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Tapestation (Agilent, Waldbronn, Germany). Median DV200 values of the included patients were 36.4% (IQR 29.4-42.7%). The SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Clontech Laboratories, Inc., A Takara Bio Company, California, USA) was used in the succeeding steps. Quality and quantity of the enriched libraries was validated using Qubit® (1.0) Fluorometer and Tapestation (Agilent, Waldbronn, Germany). The NovaSeq 6000 (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocol. For a detailed description, see Supplementary Methods.

treatment_protocol: The diagnostic kidney biopsy specimens were processed and stored as formalin-fixed and paraffin-embedded (FFPE) tissue, as routinely done at our institution. Laser capture microdissection for isolation of 10µm thick glomerular cross-sections was carried out using Leica LMD7 (Wetzlar, Germany). We collected on average 62 glomerular cross sections from each biopsy.

value: renal tissue, FFPE

tag: gender

value: Female

tag: analysis group

value: nonprog

tag: igan

value: yes


title: Del73


title: NP36

value: Male


title: TNFa3

value: endothelium

value: Human Umbilical Vein Endothelial Cells

value: WT


title: P33

value: prog


title: KO_48_rep2

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

data_processing:
Tick transcript data was downloaded from the VectorBase (https://vectorbase.org/vectorbase/app/) and indexed using the kallisto-index.
The reads from the sequencer were pseudo-aligned with the index reference transcriptome using kallisto.
The counts generated were processed by DESeq2 in RStudio (https://rstudio.com).
Assembly: IscaW1
Supplementary files format and content: tab-delimited text file includes tpm value for each gene

organism: Ixodes scapularis

source_name: Gut and salivary gland

extract_protocol:
Tick gut and salivary gland was dissected, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gut and salivary gland

value: Feeding on adiponectin knockout  mice


title: NP27


title: KO_48_rep1


title: Mock4

value: CD8+ T Cells

value: Non-infected Bovine Turbinates cells


title: Mock2-GEX

description: 10x Genomics

value: CD8+ T cells


title: Mock2


title: B2_AGY1611_Gen0_Rep3

city: Madison

description:
1611_time0_rep3
Batch2_Dutcher_barcode_cts.csv

value: North American

value: plasmid DNA


title: NP24


title: B2_AGY1613_Gen5_Rep1

description:
1613_5gen_rep1
Batch2_Dutcher_barcode_cts.csv


title: WT_48_rep2

value: Feeding on adiponectin wildtype  mice


title: B2_AGY1611_Gen0_Rep1

description:
1611_time0_rep1
Batch2_Dutcher_barcode_cts.csv


title: P22

value: renal tissue, FFPE


title: WT-718

value: Bovine Turbinates Cells infected with WT strain of AlHV-1


title: WT_48_rep1


title: WT15

data_processing:
Reads were mapped to the NCBI Bos taurus Annotation Release 106 and the AlHV-1 BAC genome from (KX905135.1) using STAR.
Subsequently the analysis was performed with R Bioconductor packages Rsamtools  and GenomicAlignments were used to count the reads by exons, and gene count datasets were then analyzed to determine differentially expressed genes (DEGs) using DESeq2.
Assembly: bosTau9
Supplementary files format and content: row count text file per sample

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were subjected to a microbead-based negative selection protocol. Total RNA was purified from 2 millions of CD8+ T lymphocytes using an RNeasy Mini Kit. A total of 1 μg of total RNA was used as input for the Truseq stranded mRNA sample kit (Illumina)
A total of 1 μg of total RNA was used as input for the Truseq stranded mRNA sample kit (Illumina)

value: Peripheral blood mononuclear cells


title: B2_AGY1611_Gen5_Rep2

description:
1611_5gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: B2_AGY1611_Gen5_Rep3

description:
1611_5gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: WT14


title: B2_AGY1611_Gen5_Rep1

description:
1611_5gen_rep1
Batch2_Dutcher_barcode_cts.csv


title: B2_AGY1611_Gen10_Rep3

description:
1611_10gen_rep3
Batch2_Dutcher_barcode_cts.csv


title: P15

value: yes


title: WT-15


title: P14

value: Male


title: B2_AGY1611_Gen0_Rep2

description:
1611_time0_rep2
Batch2_Dutcher_barcode_cts.csv


title: WT12


title: NP09

value: nonprog


title: B2_AGY1611_Gen10_Rep2

description:
1611_10gen_rep2
Batch2_Dutcher_barcode_cts.csv


title: P08

value: Female


title: WT11


title: P23


title: WT10


title: WT-911


title: NP16


title: GFKO Colon D0_6

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

description:
Gene expression at day 0 before induction of DSS colitis
GFKo6col

hyb_protocol: Samples were hybridized to SurePrint G3 mouse GE v2 8x60K (G4852B-074809) arrays and scanned by G2565CA Scanner System (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the  Agilent DNA Microarray Scanner (G2505C) using one color scan setting for  1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye  channel is set to Green and Green PMT is set to 100%).

data_processing: Image analyses and raw signal intensities were  quantified by Feature Extraction Software v10.7.3.1 (Agilent Technologies)  according to the GE1_107_Sep09 protocol.

source_name: Germ Free Colon

label_protocol: Labelling of total RNA (100ng) was performed with the One-Color Low Input Quick Amp Labelling kit (Agilent Technologies).

extract_protocol: Total RNA was prepared from total tissue of colon by using the column-based RNeasy® Mini Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples with RNA integrity number (RIN) greater than 9 were selected for further analysis.

treatment_protocol: To induce colitis, mice were administered drinking water supplemented with 2% (wt./vol.) dextran sulfate sodium (DSS; MP Biomedicals, LLC, Aurora, OH, USA) for 7 d and were then allowed to recover by drinking unsupplemented water for the next 5 d

value: Colon

value: male

tag: stran

value: Germ-free Card9−/− C57BL/6J

value: DSS

tag: time


title: P06

tag: tissue

value: prog


title: WT13

tag: cell type

value: CD8+ T Cells


title: B1_AGY1613_Gen10_RepD

description:
GaschNuSeq_1031
Batch1_Dutcher_barcode_cts.csv


title: Del8

tag: treatment

value: Bovine Turbinates Cells infected with ORF73-deficient strain of AlHV-1


title: WT-617


title: GFKO Colon D0_5

description:
Gene expression at day 0 before induction of DSS colitis
GFKo5col


title: NP04


title: B2_AGY1611_Gen10_Rep1

description:
1611_10gen_rep1
Batch2_Dutcher_barcode_cts.csv

tag: strain

value: North American


title: Del6


title: B1_AGY1612_Gen10_RepD

description:
GaschNuSeq_1030
Batch1_Dutcher_barcode_cts.csv

tag: genetic lineage

value: plasmid DNA


title: NP02


title: Del5


title: B1_AGY1611_Gen10_RepD

description:
GaschNuSeq_1029
Batch1_Dutcher_barcode_cts.csv

tag: generation


title: GFWT Colon D0_6

description:
Gene expression at day 0 before induction of DSS colitis
GFWT6col

value: Germ-free C57BL/6J WT


title: B1_AGY1614_Gen0_RepD

description:
GaschNuSeq_1028
Batch1_Dutcher_barcode_cts.csv

tag: media


title: NP01

value: renal tissue, FFPE


title: B1_AGY1613_Gen0_RepD

description:
GaschNuSeq_1027
Batch1_Dutcher_barcode_cts.csv


title: Mock4

value: Non-infected Bovine Turbinates cells


title: B1_AGY1614_Gen10_RepD

description:
GaschNuSeq_1032
Batch1_Dutcher_barcode_cts.csv


title: P07


title: GFKO Colon D0_4

description:
Gene expression at day 0 before induction of DSS colitis
GFKo4col


title: Del7

value: Peripheral blood mononuclear cells


title: B1_AGY1612_Gen0_RepD

description:
GaschNuSeq_1026
Batch1_Dutcher_barcode_cts.csv


title: GFWT Colon D0_4

description:
Gene expression at day 0 before induction of DSS colitis
GFWT4col


title: NCI-H226 cells, TM2, 2

city: Charlestown

first: Yang

last: Sun

state: MA

address: 149 13th Street, CBRC 3050E

department: CBRC

institute: Massachusetts General Hospital

data_processing:
"Qphred" represents base quality values of Illunima, the Qphred=-10log10(e). Base Quality and Phred score relationship in illumina Casava 1.8
GC-content is used to detect potential AT/GC separation.
The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Novogene use STAR to accomplish the mapping. For the spieces(Human and mice) whose gene annotation information are more completed, if only need the differential expression significant genes, can map reads to the transcriptome directly. If research the study of alternative splicing, variation, the fusion gene, the alignment should be carried out at the genome level. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely
Reads will be mapped to exon, intron and intergenic.
After getting the information about distribution of mapped reads on genome area, we will focus the distribution of mapped reads on chromosome. On one hand we can get insight into how many regions on chromosome is covered, on the other hand we can get the information about transcription activity on chromosome.We calculate mapped reads density on every chromosome , then plot based on the mapped reads density. In general, the longer the chromosome is, the more reads will be mapped to the chromosome. The statistics of reads mapped to chromosome indicates the relationship between chromosome length and reads number.
Assembly: hg19
Supplementary files format and content: fpkm

growth_protocol: NCI-H226 cells were culture in RPMI supplied with 10% FBS and Penicillin-Streptomycin

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen 74104)
mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer.Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Cells were treated with vehicle control or TM2(1uM) for 24 hours

tag: cell line

value: Mesothelioma cell

tag: genotype

value: WT

value: TM2 1μM

value: 24 hours


title: Mock3


title: NCI-H226 cells, TM2, 1


title: GFKO Colon D0_1

description:
Gene expression at day 0 before induction of DSS colitis
GFKo1col

value: Colon


title: Mock2


title: GFWT Colon D0_5

description:
Gene expression at day 0 before induction of DSS colitis
GFWT5col

value: male


title: NCI-H226 cells, Control, 2

value: vehicle control


title: GFWT Colon D0_3

description:
Gene expression at day 0 before induction of DSS colitis
GFWT3col

value: DSS


title: B1_AGY1611_Gen0_RepD

description:
GaschNuSeq_1025
Batch1_Dutcher_barcode_cts.csv

data_processing:
library strategy: BAR-seq
Read counts generated using a script to identify samples from fastq files that are associated with each 10bp index tag
Assembly: YPS1009
Supplementary files format and content: Raw Count data, csv files

tag: molecule type


title: Mock1


title: GFKO Colon D0_3

description:
Gene expression at day 0 before induction of DSS colitis
GFKo3col

value: Germ-free Card9−/− C57BL/6J


title: NCI-H226 cells, Control, 1


title: B1_AGY1614_Gen10_RepC

description:
GaschNuSeq_1024
Batch1_Dutcher_barcode_cts.csv


title: B1_AGY1612_Gen10_RepC

description:
GaschNuSeq_1022
Batch1_Dutcher_barcode_cts.csv


title: HepG2 PQY23_1_3

city: Guangzhou

first: Lan

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

data_processing:
Cutadapt software (version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare. software(version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2,and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count or log2FPKM values for each Sample …

source_name: human liver carcinoma cells

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human liver carcinoma cells


title: B1_AGY1611_Gen10_RepC

description:
GaschNuSeq_1021
Batch1_Dutcher_barcode_cts.csv


title: HepG2 PQY23_1_2


title: HF_Female_5

city: Bellinzona

first: Marco

last: Bolis

address: Via Francesco Chiesa

institute: IOR Institute of Oncology Research

data_processing:
The overall quality of sequencing reads was evaluated using FastQC. Alignments to the reference mouse genome (GRCm38.p6) were performed using STAR (v.2.6.1c) in two-pass mode. Gene expression was quantified at the gene level by using the comprehensive annotations made available by Gencode (M25). Samples were adjusted for library size and normalized with the variance stabilizing transformation in the R statistical environment using DESeq2 (v1.28.1).
Assembly: GRCm38.p6
Supplementary files format and content: tab delimited raw count matrix, quantified at the gene level by using Gencode (M25 GTF-File) and STAR (v.2.6.1c)

source_name: Gastrocnemius Muscle

extract_protocol:
RNA was isolated with TRIzol reagent (Sigma-Aldrich) and purified using the Direct-zol RNA MiniPrep Kit (Zymo Research) according to the manufacturer's protocol.
RNA integrity was checked with Agilent 2100 Bioanalyzer system. Protocol used was NEBNext rRNA depletion KIT. Sequencing of the libraries was performed using the NextSeq 500 with the NextSeq 500/550 High Output Kit v2 (75 cycles; Illumina).

treatment_protocol: Haenkenium extract was administered at the dosage of 0.5 mg/kg/day in drinking water. Mice treatment started at 20 months of age. HK extract was replaced and prepared fresh on a weekly basis.

value: Gastrocnemius Muscle

tag: Sex

value: Female

value: Haenkenium extract

tag: treatment dose

tag: experimental batch


title: B1_AGY1614_Gen0_RepC

description:
GaschNuSeq_1020
Batch1_Dutcher_barcode_cts.csv

extract_protocol:
Plasmids were recovered from each pool using Zymoprep Yeast Plasmid Miniprep II (Zymo Research D2004-A) with the following modifications: samples were incubated with 15 units zymolyase at 37°C for 1 hour, with inversion every 15 minutes; incubation in cell lysis buffer was extended to 10 minutes; after neutralization, samples were put on ice for 30 minutes, then centrifuged at 4°C.
Plasmid barcodes were amplified using primers containing Illumina multiplex adaptors as described in (Piotrowski et al. 2015), with number of PCR cycles reduced to 20. Barcode amplicons were pooled and purified using AxyPrep Mag beads (1.8X volume beads per sample volume) according to the manufacturer’s instructions (Axygen).

value: North American

value: plasmid DNA


title: HepG2 PQY23_1_1


title: HF_Female_4

value: Haenkenium extract was administered at the dosage of 0.5 mg/kg/day in drinking water


title: A4_1

city: Shanghai

first: Yanting

last: Shen

address: Miaopu road 219

department: Department of Urology and andrology

institute: Gongli Hospital, the Second Military Medical University

description: 10x Genomics

data_processing:
FASTQ files were processed to generate the feature barcode (FB) matrices by using spaceranger software (version 1.1.0) according to Space Ranger pipeline. FB matrices were loaded in the R package Seurat (Version 3.0.0) for subsequent analysis.
Assembly: hg18
Library strategy: spatial transcriptomics

source_name: prostate

extract_protocol:
Cryosection from an OCT-embedded BPH tissue sample was placed on Visium spatial slide. The mRNA molecules bound by printed capture oligos, which contained spatial barcodes on the slide, were converted into cDNA.
Spatial libraries were constructed using the Visium Spatial Library Construction Kit (10x Genomics, PN-1000184).

value: prostate

tag: disease state

value: benign prostatic hyperplasia


title: HepG2 PQY09_3

value: 50uM PQY09


title: B1_AGY1613_Gen10_RepC

description:
GaschNuSeq_1023
Batch1_Dutcher_barcode_cts.csv


title: GFWT Colon D0_2

description:
Gene expression at day 0 before induction of DSS colitis
GFWT2col

tag: gender

value: Germ-free C57BL/6J WT


title: HF_Female_3


title: HepG2 PQY09_2


title: HepG2 PQY09_1


title: B1_AGY1612_Gen0_RepC

description:
GaschNuSeq_1018
Batch1_Dutcher_barcode_cts.csv


title: HF_Female_2


title: B1_AGY1611_Gen0_RepC

description:
GaschNuSeq_1017
Batch1_Dutcher_barcode_cts.csv


title: GFKO Colon D0_2

description:
Gene expression at day 0 before induction of DSS colitis
GFKo2col

tag: stran


title: GFKO Colon D0_7

description:
Gene expression at day 0 before induction of DSS colitis
GFKo7col

tag: time


title: HF_Female_1

tag: tissue


title: HepG2 ctrl_3

value: 0.1% DMSO


title: GFWT Colon D0_1

description:
Gene expression at day 0 before induction of DSS colitis
GFWT1col

value: Colon


title: HK_Male_5

value: Male


title: B1_AGY1614_Gen10_RepB

description:
GaschNuSeq_1016
Batch1_Dutcher_barcode_cts.csv


title: DSCL cases 3

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

country: United Kingdom

institute: The University of Sheffield

description: DSCL case

hyb_protocol: Approximately 5.5 μg amplified cDNA was fragmented, labelled and hybridised to Clariom S Array chips for 16 h at 45 °C in a rotating oven at 60 rpm.

scan_protocol: Using the Fluidics Station 400 and GeneChip Operating System, a series of washing steps followed to remove any unbound DNA, before each microarray was stained and scanned using the GeneChip 3000 scanner.

data_processing: Affymetrix Expression Console software (Affymetrix®, Stockport, UK) was employed to quality control the data and principal component analysis (PCA) in Qlucore Omics Explorer software (Qlucore, Lund, Sweden) was used to visually inspect the data and identify sample outliers. Transcriptome Analysis Console (TAC) software, version 4.1.1 (Affymetrix®, UK) was used to analyse and compare the gene expression profile of the 3 groups.

source_name: Human post-mortem tissue

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted from the LCM-isolated cells using the PicoPure RNA isolation kit (Life technologies: Applied Biosystems, USA).

tag: age (yrs)


title: DSCL cases 2

description: DSCL case


title: NAWM matched with the DSCL cases 4

description: NAWM case


title: HepG2 ctrl_2

tag: treatment


title: DSCL cases 4

description: DSCL case


title: B1_AGY1613_Gen10_RepB

first: Audrey

address: 425G Henry mall

institute: University of Wisconsin

description:
GaschNuSeq_1015
Batch1_Dutcher_barcode_cts.csv

tag: strain


title: DSCL cases 1

description: DSCL case


title: NAWM matched with the DSCL cases 3

description: NAWM case


title: B1_AGY1613_Gen0_RepC

description:
GaschNuSeq_1019
Batch1_Dutcher_barcode_cts.csv

tag: genetic lineage


title: NAWM matched with the DSCL cases 2

description: NAWM case


title: HepG2 ctrl_1


title: HK_Male_3


title: B1_AGY1611_Gen10_RepB

description:
GaschNuSeq_1013
Batch1_Dutcher_barcode_cts.csv

tag: generation


title: HK_Male_2


title: M2a_F_16C5_D3

city: South San Francisco

first: Joshua

last: Lichtman

state: CA

address: 333 Oyster Point Boulevard

department: Translational Science

institute: NGM Biopharmaceuticals

data_processing:
Data raw reads were filtered using Trim Galore! to remove low quality and adaptor bases. Reads shorter than 20nt were discarded.
Filtered reads were mapped to UCSC hg19 genome sequences using STAR (v2.6.0a).
At last, counts of all samples were generated using featureCounts (v1.6.2), and edgeR (v3.22.3) was used to get normalized counts and perform differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression raw read counts in tabular data format

source_name: M2a macs, fibronectin and 16C5 antibody treatment

extract_protocol:
Cells were harvested in TRIzol and RNA was isolated by choroform extraction, follwed by purification with the Rneasy kit (Qiagen).
Total RNA was prepared for sequencing using the TailorMix Directional RNA Sample Preparation Kit (SeqMatic) and sequenced on an Illumina NovaSeq S1.

treatment_protocol: Peripheral blood monocytes from healthy human donors were plated on wells pre-coated with PBS or fibronectin (5 ug/mL) in the presence of an anti-KLH control antibody or anti-ILT3 16C5 (10 ug/mL). Monocytes were differentiated into dendritic cells or macrophages as follows: Monocyte-derived DCs (GM-CSF/IL-4 for 7 days), tolerogenic DCs (GM-CSF/IL-4 for 5 days + vitamin D3/dexamethasone for 2 days), or macrophages (M-CSF for 5 days plus IFN-g/LPS for 2 days for M1 macrophages, IL-4 for 2 days for M2a macrophages, or IL-10 for 2 days for M2c macrophages).

tag: cell type

value: M2a macrophage

tag: plate coating

value: Fibronectin

tag: donor

value: Donor 3

tag: antibody treatment

value: anti-ILT3 16C5


title: M2c_F_16C5_D3

source_name: M2c macs, fibronectin and 16C5 antibodoy treatment

value: M2c macrophage


title: Control WML  3

description: Control case


title: Control WML  4

description: Control case

value: Female


title: M1_F_16C5_D3

source_name: M1 macs, fibronectin and 16C5 antibody treatment

value: M1 macrophage


title: Control WML  2

description: Control case


title: B1_AGY1612_Gen0_RepB

last: Gasch

description:
GaschNuSeq_1010
Batch1_Dutcher_barcode_cts.csv

value: North American

tag: media

tag: molecule type


title: B1_AGY1611_Gen0_RepB

description:
GaschNuSeq_1009
Batch1_Dutcher_barcode_cts.csv

value: plasmid DNA


title: O, snRNA-seq

city: Nantong

first: Yinchuan

last: Li

state: Jiangsu

address: 16 wenfeng road, Chongchuan

department: Medical School

institute: Nantong University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger V3.1.0. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger )
Assembly: Ensembl_release104
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: hypothalamus

extract_protocol:
Intact hypothalami were cryopreserved in liquid nitrogen from sacrificed rats and approximately 2-3 pooled intact hypothalami in each group were homogenized in 500µL ice-cold homogenization buffer (0.25 M sucrose, 5 mM CaCl2 , 3 mM MgAc2, 10 mM Tris-HCl pH 8.0, 1 mM DTT, 0.1 mM EDTA, 1x protease inhibitor, and 1 U µL−1 RiboLock RNase inhibitor) with Dounce homogenizer. Then the homogenizer was washed with 700µL ice-cold nuclei washing buffer (0.04% bovine serum albumin, 0.2 U/µL RiboLock RNase Inhibitor, 500 mM mannitol, 0.1 mM phenylmethanesulfonyl fluoride Protease Inhibitor in 1 x PBS). Next, the homogenates were filtered through a 70 µm cell strainer to collect the nuclear fraction. The nuclear fraction was mixed with an equal volume of 50% iodixanol and added on top of a 30% and 33% iodixanol gradient. This solution was then centrifuged for 20 min at 10 000 ×g at 4 °C. After the myelin layer was removed from the top of the gradient, the nuclei were collected from the 30% and 33% iodixanol interface. The nuclei were resuspended in nuclear wash buffer and resuspension buffer and pelleted for 5 min at 500 ×g at 4 °C. The nuclei were filtered through a 40 µm cell strainer to remove cell debris and large clumps and the nuclear concentration was manually assessed using trypan blue counterstaining and a hemocytometer. Finally, the nuclei were adjusted to 700–1200 nuclei µL−1, and examined with a 10X Chromium platform.
Reverse transcription, cDNA amplification and library preparation were performed based on the protocol from 10X Genomics. Briefly, nuclei were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 5’ Reagent Kits v3.1. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers which were used in Illumina bridge amplification. The Single Cell 5’ Protocol produced Illumina-ready sequencing libraries. A Single cell 5’ library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 5’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing. Library sequencing was performed on the Illumina HiseqTM 4000 by Gene Denovo Biotechnology Co., Ltd (Guangzhou, China).

value: hypothalamus

tag: Sex

value: male

value: no treatment

tag: age

value: 30 months


title: B1_AGY1612_Gen10_RepB

description:
GaschNuSeq_1014
Batch1_Dutcher_barcode_cts.csv


title: CTRL_Female_2

value: Gastrocnemius Muscle

value: untreated

tag: treatment dose

value: drinking water

tag: experimental batch


title: CTRL_Female_4


title: Y, snRNA-seq

description: 10X Genomics

value: 4 months


title: B1_AGY1614_Gen0_RepB

description:
GaschNuSeq_1012
Batch1_Dutcher_barcode_cts.csv


title: Control WML  1

description: Control case

tag: gender


title: tolDC_F_16C5_D3

source_name: TolDCs, fibronectin and 16C5 antibody treatment

value: Tolerogenic DC


title: B1_AGY1613_Gen0_RepB

description:
GaschNuSeq_1011
Batch1_Dutcher_barcode_cts.csv


title: M0_F_16C5_D3

source_name: M0 macs, fibronectin and 16C5 antibody treatment

value: M0 macrophage

value: Fibronectin